Myujth

I am having trouble importing a specific package using reticulate within R (Feather Spray, version 3.5.1) and RStudio (version 1.1.456) on my MacBook Pro running High Sierra. The Python module I'm working with is called RDKit (https://github.com/rdkit/rdkit). The package works fine on the same computer when importing from the Python command line (or Spyder for that matter) as follows:

>>> import rdkit
import rdkit # directory /Users/pleeferguson/apps/rdkit/rdkit
# /Users/pleeferguson/apps/rdkit/rdkit/__init__.pyc matches /Users/pleeferguson/apps/rdkit/rdkit/__init__.py
import rdkit # precompiled from /Users/pleeferguson/apps/rdkit/rdkit/__init__.pyc
dlopen("/Users/pleeferguson/apps/rdkit/rdkit/rdBase.so", 2);
import rdkit.rdBase # dynamically loaded from /Users/pleeferguson/apps/rdkit/rdkit/rdBase.so
>>>

When I try to import RDKit within RStudio using reticulate, it fails as follows:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")
> library(reticulate)
> rdkit <- import_from_path("rdkit", "/Users/pleeferguson/apps/rdkit/rdkit")
Error in py_module_import(module, convert = convert) : 
 ImportError: No module named rdBase
> 

I also tried to import the module directly within R from the terminal (outside of RStudio), where I received a more informative error message:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")
> library(reticulate)
> rdkit <- import("rdkit")
Error in py_module_import(module, convert = convert) : 
 ImportError: dlopen(/Users/pleeferguson/apps/rdkit/rdkit/rdBase.so, 2): Library not loaded: @rpath/libRDKitRDBoost.1.dylib
 Referenced from: /Users/pleeferguson/apps/rdkit/rdkit/rdBase.so
 Reason: image not found

Detailed traceback: 
 File "/Users/pleeferguson/apps/rdkit/rdkit/__init__.py", line 2, in <module>
 from .rdBase import rdkitVersion as __version__
>

I've verified that there is indeed a symlink named libRDKitRDBoost.1.dylib at the right place and pointing to the correct dylib file (it does exist within the lib directory of the RDKit package).

Also, I have no trouble importing other packages (e.g. pandas) within RStudio using reticulate:

> reticulate::use_python("/Library/Frameworks/Python.framework/Versions/2.7/bin/python")
> library(reticulate)
> pd <- import("pandas", as = "pd")
> 

On my other MacBook Pro with an earlier version of both R (Sincere Pumpkin Patch) and RDKit (2015 build), the rdkit package loads just fine (and is functional) from within RStudio, using reticulate.

Any ideas what might be happening here? I don't think it is an RStudio issue, as I've tried installing the newest daily build of RStudio but get the same behavior. Also, the fact that I can't get the package to import from R within the terminal (outside of RStudio) tells me it must be something else.